Abstract The freezing behavior of copper nanowires at different cooling rates was studied by using molecular dynamics (MD) simulation via embedded atom methods (EAM) potential. The simulation results indicate that the structure of the nanowires changed from amorphous to crystalline via helical multi-shelled structure with decreasing cooling rates. The curves of the energy-temperature and the local clusters were used to study the phase transition. The variation of local clusters implies that the order of the system increases as the temperature drops. The fcc crystalline structure of the copper nanowires with the diameter of 1.63 nm was proved to be the most stable form.